[Bioc-devel] add function to "annotate" package

[Robert M. Flight]

Would it make sense to add one extra level of convenience to the
"getAnnMap" function in "annotate", that represents what I am sure is
one of the largest number of uses of the bimaps as an environment,
which is getting information about a particular set of genes or other
identifier?

getAnnotation <- function(id,annPackage,mapID,doUnlist=TRUE){
	annEnv <- getAnnMap(mapID, annPackage, load=TRUE)
  tmpDat <- mget(id, annEnv, ifnotfound=NA)
  if (doUnlist){
  	tmpDat <- unlist(tmpDat, use.names=FALSE)
  }
  return(tmpDat)
}

# simple example, but I do this for a lot of different things frequently
library(annotate)
testEntrez <- c("1","10","100","1000")
getAnnotation(testEntrez,"org.Hs.eg.db","SYMBOL")

Thanks,

-Robert

Robert M. Flight, Ph.D.
University of Louisville Bioinformatics Laboratory
University of Louisville
Louisville, KY

PH 502-852-1809 (HSC)
PH 502-852-0467 (Belknap)
EM robert.flight at louisville.edu
EM rflight79 at gmail.com

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